And since neither stopbadware nor Google have made it apparent what the determining factors are, I have to believe that there is something else going on that gets a site listed as such.

Your advice on content optimization is spot on. I do want to clear up one thing though. You said that “Sometimes sites get listed on stopbadware.org just because their JavaScript doesn’t work correctly, or advertising doesn’t load properly.” As a representative of StopBadware, I want to assure you and your readers that that is not the case. At present, the badware sites listed in StopBadware’s Clearinghouse are all independently flagged by Google, and Google is responsible for placing warnings for malware in its own search results. Google’s determinations are entirely based on its findings of badware, links to badware, or badware-distributing code such as exploits. While simply poorly coded or poorly validated sites may lose some points from Google (I can’t speak to their normal search algorithms at all), that would never alone be a cause for a badware warning.

We have more information about the warnings, and StopBadware’s involvement, here:
http://www.stopbadware.org/home/faq#partnerwarnings

Erica
StopBadware staff